Significance A reservoir of latently infected cells poses the greatest challenge to HIV-1 eradication. Efforts to develop strategies to eliminate the reservoir have been hampered, in part, by the lack of a precise understanding of the cellular and molecular nature of this reservoir. We describe a new method to analyze the replication-competent latent reservoir quantitatively and qualitatively. We find that over 50% of the replication-competent viruses in the reservoir form part of groups with identical env sequences. However, a negative correlation exists between integrated proviral clones and replication-competent viruses, such that the larger the proviral clone, the lower is its probability of representing a replication-competent virus.